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Fusion gene ID: 35175 |
FusionGeneSummary for SNRNP40_PEF1 |
Fusion gene summary |
Fusion gene information | Fusion gene name: SNRNP40_PEF1 | Fusion gene ID: 35175 | Hgene | Tgene | Gene symbol | SNRNP40 | PEF1 | Gene ID | 9410 | 553115 |
Gene name | small nuclear ribonucleoprotein U5 subunit 40 | penta-EF-hand domain containing 1 | |
Synonyms | 40K|HPRP8BP|PRP8BP|PRPF8BP|SPF38|WDR57 | ABP32|PEF1A | |
Cytomap | 1p35.2 | 1p35.2 | |
Type of gene | protein-coding | protein-coding | |
Description | U5 small nuclear ribonucleoprotein 40 kDa protein38 kDa-splicing factorPrp8-binding proteinU5 snRNP 40 kDa proteinU5 snRNP-specific 40 kDa protein (hPrp8-binding)U5-40KU5-40kD proteinWD repeat domain 57 (U5 snRNP specific)WD repeat-containing prot | peflinPEF protein with a long N-terminal hydrophobic domain | |
Modification date | 20180523 | 20180522 | |
UniProtAcc | Q96DI7 | Q9UBV8 | |
Ensembl transtripts involved in fusion gene | ENST00000263694, ENST00000489853, ENST00000373720, ENST00000446633, | ENST00000373703, ENST00000492061, ENST00000440872, | |
Fusion gene scores | * DoF score | 6 X 3 X 5=90 | 1 X 1 X 1=1 |
# samples | 5 | 1 | |
** MAII score | log2(5/90*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(1/1*10)=3.32192809488736 | |
Context | PubMed: SNRNP40 [Title/Abstract] AND PEF1 [Title/Abstract] AND fusion [Title/Abstract] | ||
Functional or gene categories assigned by FusionGDB annotation |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Partner | Gene | GO ID | GO term | PubMed ID |
Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
TCGA | RV | UCEC | TCGA-H5-A2HR-01A | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
* LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
In-frame | ENST00000263694 | ENST00000373703 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
5CDS-5UTR | ENST00000263694 | ENST00000492061 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
5CDS-5UTR | ENST00000263694 | ENST00000440872 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-3CDS | ENST00000489853 | ENST00000373703 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-5UTR | ENST00000489853 | ENST00000492061 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-5UTR | ENST00000489853 | ENST00000440872 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-3CDS | ENST00000373720 | ENST00000373703 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-5UTR | ENST00000373720 | ENST00000492061 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
intron-5UTR | ENST00000373720 | ENST00000440872 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
Frame-shift | ENST00000446633 | ENST00000373703 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
5CDS-5UTR | ENST00000446633 | ENST00000492061 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
5CDS-5UTR | ENST00000446633 | ENST00000440872 | SNRNP40 | chr1 | 31762101 | - | PEF1 | chr1 | 32101123 | - |
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FusionProtFeatures for SNRNP40_PEF1 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
SNRNP40 | PEF1 |
Component of the U5 small nuclear ribonucleoprotein(snRNP) complex. The U5 snRNP is part of the spliceosome, amultiprotein complex that catalyzes the removal of introns frompre-messenger RNAs. {ECO:0000269|PubMed:9774689}. | Calcium-binding protein that acts as an adapter thatbridges unrelated proteins or stabilizes weak protein-proteincomplexes in response to calcium. Together with PDCD6, acts ascalcium-dependent adapter for the BCR(KLHL12) complex, a complexinvolved in endoplasmic reticulum (ER)-Golgi transport byregulating the size of COPII coats (PubMed:27716508). In responseto cytosolic calcium increase, the heterodimer formed with PDCD6interacts with, and bridges together the BCR(KLHL12) complex andSEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31and subsequent collagen export, which is required for neural crestspecification (PubMed:27716508). Its role in the heterodimerformed with PDCD6 is however unclear: some evidences show thatPEF1 and PDCD6 work together and promote association between PDCD6and SEC31 in presence of calcium (PubMed:27716508). Other reportsshow that PEF1 dissociates from PDCD6 in presence of calcium, andmay act as a negative regulator of PDCD6 (PubMed:11278427). Alsoacts as a negative regulator of ER-Golgi transport; possibly byinhibiting interaction between PDCD6 and SEC31 (By similarity).{ECO:0000250|UniProtKB:Q641Z8, ECO:0000269|PubMed:11278427,ECO:0000269|PubMed:27716508}. |
Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
- In-frame and retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Hgene | SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 107_146 | 177 | 358 | Repeat | Note=WD 2 |
Hgene | SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 64_103 | 177 | 358 | Repeat | Note=WD 1 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 127_138 | 8 | 285 | Calcium binding | 1 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 194_205 | 8 | 285 | Calcium binding | 2 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 114_149 | 8 | 285 | Domain | EF-hand 1 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 155_183 | 8 | 285 | Domain | EF-hand 2 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 181_216 | 8 | 285 | Domain | EF-hand 3 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 217_253 | 8 | 285 | Domain | EF-hand 4 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 254_283 | 8 | 285 | Domain | EF-hand 5 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 21_109 | 8 | 285 | Region | 9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 101_109 | 8 | 285 | Repeat | 9 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 21_29 | 8 | 285 | Repeat | 1 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 31_39 | 8 | 285 | Repeat | 2 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 41_49 | 8 | 285 | Repeat | 3 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 50_58 | 8 | 285 | Repeat | 4 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 59_67 | 8 | 285 | Repeat | 5 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 76_84 | 8 | 285 | Repeat | 6 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 85_92 | 8 | 285 | Repeat | 7 |
Tgene | >PEF1 | chr1:31762101 | chr1:32101123 | ENST00000373703 | - | 0 | 5 | 93_100 | 8 | 285 | Repeat | 8 |
- In-frame and not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Hgene | >SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 149_189 | 177 | 358 | Repeat | Note=WD 3 |
Hgene | >SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 191_230 | 177 | 358 | Repeat | Note=WD 4 |
Hgene | >SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 233_272 | 177 | 358 | Repeat | Note=WD 5 |
Hgene | >SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 283_322 | 177 | 358 | Repeat | Note=WD 6 |
Hgene | >SNRNP40 | chr1:31762101 | chr1:32101123 | ENST00000263694 | - | 4 | 10 | 325_357 | 177 | 358 | Repeat | Note=WD 7 |
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FusionGeneSequence for SNRNP40_PEF1 |
For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
* Fusion amino acid sequences. |
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_454aa MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIMLLSGHEGEVYCCKFHPNGSTLASAGFDRLI LLWNVYGDCDNYATLKGHSGAVMELHYNTDGSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKGCP GAAGQAPGAPPGSYYPGPPNSGGQYGSGLPPGGGYGGPAPGGPYGPPAGGGPYGHPNPGMFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQ QPGLYGQGGAPPNVDPEAYSWFQSVDSDHSGYISMKELKQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQ QYDRDRSGSISYTELQQALSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVTMTAS |
* Fusion transcript sequences (only coding sequence (CDS) region). |
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_1362nt ATGATAGAACAGCAGAAGCGTAAGGGCCCAGAGTTGCCGCTGGTTCCAGTCAAGCGGCAGCGGCATGAGTTGCTGTTGGGAGCGGGGTCT GGCCCAGGAGCCGGGCAGCAGCAGGCGACGCCGGGAGCCTTGCTGCAAGCGGGACCTCCAAGATGTTCCTCCCTTCAAGCCCCAATCATG CTGCTCTCTGGACATGAAGGGGAAGTCTACTGCTGCAAGTTCCACCCCAACGGATCCACCTTAGCATCTGCAGGATTTGACCGACTGATA TTACTGTGGAATGTCTATGGTGACTGTGATAACTATGCCACACTGAAGGGACACAGTGGAGCAGTGATGGAATTGCATTACAACACAGAT GGCAGTATGCTTTTCTCAGCATCCACAGATAAAACCGTGGCTGTGTGGGATAGTGAAACAGGTGAGAGGGTTAAAAGGCTAAAGGGACAT ACTTCCTTTGTGAATTCCTGTTATCCAGCCAGGAGAGGCCCTCAGCTTGTCTGCACTGGCAGTGACGATGGCACAGTTAAGGGCTGCCCA GGAGCTGCAGGACAAGCACCAGGAGCCCCTCCGGGTAGCTACTACCCTGGACCCCCCAATAGTGGAGGGCAGTATGGTAGTGGGCTACCC CCTGGTGGTGGTTATGGGGGTCCTGCCCCTGGAGGGCCTTATGGACCACCAGCTGGTGGAGGGCCCTATGGACACCCCAATCCTGGGATG TTCCCCTCTGGAACTCCAGGAGGACCATATGGCGGTGCAGCTCCCGGGGGCCCCTATGGTCAGCCACCTCCAAGTTCCTACGGTGCCCAG CAGCCTGGGCTTTATGGACAGGGTGGCGCCCCTCCCAATGTGGATCCTGAGGCCTACTCCTGGTTCCAGTCGGTGGACTCAGATCACAGT GGCTATATCTCCATGAAGGAGCTAAAGCAGGCCCTGGTCAACTGCAATTGGTCTTCATTCAATGATGAGACCTGCCTCATGATGATAAAC ATGTTTGACAAGACCAAGTCAGGCCGCATCGATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGAACCTCTTCCAG CAGTATGACCGGGACCGCTCGGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTACAACCTGAGCCCCCAGTTC ACCCAGCTTCTGGTCTCCCGCTACTGCCCACGCTCTGCCAATCCTGCCATGCAGCTTGACCGCTTCATCCAGGTGTGCACCCAGCTGCAG GTGCTGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTCGGCTCAGCTTCGAGGACTTCGTCACCATGACAGCTTCT |
* Fusion transcript sequences (Full-length transcript). |
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_2132nt GAAGAGACCGGTTGCCGCCATGATAGAACAGCAGAAGCGTAAGGGCCCAGAGTTGCCGCTGGTTCCAGTCAAGCGGCAGCGGCATGAGTT GCTGTTGGGAGCGGGGTCTGGCCCAGGAGCCGGGCAGCAGCAGGCGACGCCGGGAGCCTTGCTGCAAGCGGGACCTCCAAGATGTTCCTC CCTTCAAGCCCCAATCATGCTGCTCTCTGGACATGAAGGGGAAGTCTACTGCTGCAAGTTCCACCCCAACGGATCCACCTTAGCATCTGC AGGATTTGACCGACTGATATTACTGTGGAATGTCTATGGTGACTGTGATAACTATGCCACACTGAAGGGACACAGTGGAGCAGTGATGGA ATTGCATTACAACACAGATGGCAGTATGCTTTTCTCAGCATCCACAGATAAAACCGTGGCTGTGTGGGATAGTGAAACAGGTGAGAGGGT TAAAAGGCTAAAGGGACATACTTCCTTTGTGAATTCCTGTTATCCAGCCAGGAGAGGCCCTCAGCTTGTCTGCACTGGCAGTGACGATGG CACAGTTAAGGGCTGCCCAGGAGCTGCAGGACAAGCACCAGGAGCCCCTCCGGGTAGCTACTACCCTGGACCCCCCAATAGTGGAGGGCA GTATGGTAGTGGGCTACCCCCTGGTGGTGGTTATGGGGGTCCTGCCCCTGGAGGGCCTTATGGACCACCAGCTGGTGGAGGGCCCTATGG ACACCCCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACCATATGGCGGTGCAGCTCCCGGGGGCCCCTATGGTCAGCCACCTCC AAGTTCCTACGGTGCCCAGCAGCCTGGGCTTTATGGACAGGGTGGCGCCCCTCCCAATGTGGATCCTGAGGCCTACTCCTGGTTCCAGTC GGTGGACTCAGATCACAGTGGCTATATCTCCATGAAGGAGCTAAAGCAGGCCCTGGTCAACTGCAATTGGTCTTCATTCAATGATGAGAC CTGCCTCATGATGATAAACATGTTTGACAAGACCAAGTCAGGCCGCATCGATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCA GTGGAAGAACCTCTTCCAGCAGTATGACCGGGACCGCTCGGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTA CAACCTGAGCCCCCAGTTCACCCAGCTTCTGGTCTCCCGCTACTGCCCACGCTCTGCCAATCCTGCCATGCAGCTTGACCGCTTCATCCA GGTGTGCACCCAGCTGCAGGTGCTGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTCGGCTCAGCTTCGAGGACTT CGTCACCATGACAGCTTCTCGGATGCTATGACCCAACCATCTGTGGAGAGTGGAGTGCACCAGGGACCTTTCCTGGCTTCTTAGAGTGAG AGAAGTATGTGGACATCTCTTCTTTTCCTGTCCCTCTAGAAGAACATTCTCCCTTGCTTGATGCAACACTGTTCCAAAAGAGGGTGGAGA GTCCTGCATCATAGCCACCAAATAGTGAGGACCGGGGCTGAGGCCACACAGATAGGGGCCTGATGGAGGAGAGGATAGAAGTTGAATGTC CTGATGGCCATGAGCAGTTGAGTGGCACAGCCTGGCACCAGGAGCAGGTCCTTGTAATGGAGTTAGTGTCCAGTCAGCTGAGCTCCACCC TGATGCCAGTGGTGAGTGTTCATCGGCCTGTTACCGTTAGTACCTGTGTTCCCTCACCAGGCCATCCTGTCAAACGAGCCCATTTTCTCC AAAGTGGAATCTGACCAAGCATGAGAGAGATCTGTCTATGGGACCAGTGGCTTGGATTCTGCCACACCCATAAATCCTTGTGTGTTAACT TCTAGCTGCCTGGGGCTGGCCCTGCTCAGACAAATCTGCTCCCTGGGCATCTTTGGCCAGGCTTCTGCCCTCTGCAGCTGGGACCCCTCA CTTGCCTGCCATGCTCTGCTCGGCTTCAGTCTCCAGGAGACAGTGGTCACCTCTCCCTGCCAATACTTTTTTTAATTTGCATTTTTTTTC |
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FusionGenePPI for SNRNP40_PEF1 |
Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
Hgene | Hgene's interactors | Tgene | Tgene's interactors |
SNRNP40 | PRPF8, SNRNP200, EFTUD2, CD2BP2, PRPF6, SNRPB2, PFDN2, MAGEA6, SF3B1, DDR1, USP39, PRPF4, CUL4A, CUL4B, WDR5, SRRM1, PML, RARA, ELAVL1, DHX16, RNU4ATAC, RNU6ATAC, APP, SNRPE, RALY, TBL1X, MDC1, EIF4A3, MAGOH, PRPF4B, RPA3, RPA2, RPA1, MOV10, NXF1, CUL7, OBSL1, SUZ12, DDX23, TSSC4, RSRC1, PRPF3, TFIP11, PAXBP1, PRPF31, SART1, ECD, SNRPD2, CCDC12, DHX38, SNRNP27, ZNHIT2, TXNL4A, AQR, SNRPD1, ISY1, RBM42, CHD3, CRNKL1, POLR3C, SREK1, XPO1, YWHAZ, USP37, SNW1, CDC5L, SNRPF, PPIE, AAR2, LMNA | PEF1 | PDCD6, H2AFX, UBC, CUL3, LAMTOR3, PDCD6IP, DAZAP2, BAG3, NR0B2, EWSR1, HGS, CALCOCO2, TFG, CEP55, KLHL12, FOXR2, KIAA0930, HIST2H2AB, FASN, ANXA11, ENO1, ETFA, GPI, SUCLG2, CEP128, CEP164, DMRTB1, NF2 |
- Retained PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
- Lost PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
- Retained PPIs, but lost function due to frame-shift fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for SNRNP40_PEF1 |
Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Tgene | PEF1 | Q9UBV8 | DB11093 | Calcium Citrate | Peflin {ECO:0000303|PubMed:10486255} | small molecule | approved |
Tgene | PEF1 | Q9UBV8 | DB11348 | Calcium Phosphate | Peflin {ECO:0000303|PubMed:10486255} | small molecule | approved |
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RelatedDiseases for SNRNP40_PEF1 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |